Magnesium in PDB 8vb9: Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em

The binding sites of Magnesium atom in the Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em (pdb code 8vb9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em, PDB code: 8vb9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:52.7 occ:1.00 OD1 A:ASP110 2.1 88.5 1.0 O A:VAL111 2.1 75.1 1.0 O2A A:DTP603 2.2 88.1 1.0 O2G A:DTP603 2.3 81.0 1.0 OD2 A:ASP185 2.4 80.9 1.0 O2B A:DTP603 2.7 85.0 1.0 CG A:ASP110 3.3 86.2 1.0 C A:VAL111 3.3 69.1 1.0 PA A:DTP603 3.6 84.1 1.0 PG A:DTP603 3.6 91.6 1.0 CG A:ASP185 3.6 82.5 1.0 PB A:DTP603 3.7 90.1 1.0 OD2 A:ASP110 3.9 84.3 1.0 O3B A:DTP603 4.0 81.5 1.0 O3A A:DTP603 4.0 70.7 1.0 N A:VAL111 4.1 63.9 1.0 CA A:GLY112 4.1 78.2 1.0 N A:GLY112 4.1 74.2 1.0 CA A:VAL111 4.3 64.8 1.0 NZ A:LYS220 4.3 93.4 1.0 C5' A:DTP603 4.3 75.4 1.0 OD1 A:ASP185 4.3 86.8 1.0 O1G A:DTP603 4.3 79.2 1.0 O5' A:DTP603 4.4 82.2 1.0 CB A:ASP110 4.5 82.9 1.0 N A:ASP113 4.5 86.2 1.0 C A:ASP110 4.5 76.2 1.0 CB A:ASP185 4.7 80.6 1.0 C A:GLY112 4.7 83.7 1.0 O3G A:DTP603 4.7 82.4 1.0 O1A A:DTP603 4.7 81.4 1.0 CB A:ALA114 4.8 74.0 1.0 MG A:MG602 4.8 81.6 1.0 N A:ALA114 4.8 71.9 1.0 CB A:VAL111 4.9 69.5 1.0 CA A:ASP110 4.9 74.0 1.0 O3' F:DG33 4.9 38.6 1.0

Magnesium binding site 2 out of 2 in the Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kinetic Intermediate States of Hiv-1 Rt Dna Synthesis Captured By Cryo-Em within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:81.6 occ:1.00 OD2 A:ASP110 2.4 84.3 1.0 NZ A:LYS220 3.4 93.4 1.0 CG A:ASP110 3.4 86.2 1.0 O3' F:DG33 3.9 38.6 1.0 OD1 A:ASP110 4.0 88.5 1.0 O2A A:DTP603 4.1 88.1 1.0 OP1 F:DG33 4.4 39.5 1.0 O5' F:DG33 4.5 35.8 1.0 C3' F:DG33 4.5 27.8 1.0 O1A A:DTP603 4.6 81.4 1.0 CB A:ASP110 4.6 82.9 1.0 CE A:LYS220 4.7 90.4 1.0 MG A:MG601 4.8 52.7 1.0 PA A:DTP603 4.8 84.1 1.0 CD A:LYS220 4.8 89.8 1.0 C5' F:DG33 4.8 25.1 1.0 P F:DG33 4.9 35.6 1.0 OD1 A:ASP186 4.9 92.8 1.0

S.Vergara, X.Zhou, U.Santiago, M.Alaoui-El-Azher, J.F.Conway, N.Sluis-Cremer, G.Calero. Structural Basis of Deoxynucleotide Addition By Hiv-1 Rt During Reverse Transcription Nat Commun V. 15 10553 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-54618-Y